If Python loads a script via a symbolic link, VS will think there are multiple versions of it. Currently I have these documents open:
The first document represents the actual location of the file and was created when I opened it from Solution Explorer.
The other two were opened by the debugger and represent the location at which Python thought the file existed. (Yes, I have a user folder on two different drives!)
PyTools should examine the path of any file it wants to open for symlinks and ensure that it opens the real location.